Variant report

Variant	rs6486431
Chromosome Location	chr11:18542227-18542228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18535996..18538848-chr11:18539751..18543150,4	MCF-7	breast:
2	chr11:18528948..18532458-chr11:18541566..18545702,3	K562	blood:
3	chr11:18538359..18545865-chr11:18546460..18550640,13	MCF-7	breast:
4	chr11:18540175..18542795-chr11:18547833..18549467,2	MCF-7	breast:
5	chr11:18539804..18546267-chr11:18546399..18550608,13	K562	blood:

Variant related genes	Relation type
ENSG00000256588	Chromatin interaction
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10500836	0.80[YRI][hapmap]
rs10832939	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832940	0.86[YRI][hapmap]
rs11024691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024718	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11600246	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11603992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12223260	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12224694	0.87[YRI][hapmap]
rs12225251	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12226584	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419063	0.80[YRI][hapmap]
rs12577346	0.83[YRI][hapmap]
rs1395319	0.82[YRI][hapmap]
rs1395320	0.84[YRI][hapmap]
rs16935476	0.92[JPT][hapmap]
rs16935482	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16935488	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16935538	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16935539	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292176	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802966	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3925781	0.80[YRI][hapmap]
rs4298881	0.80[YRI][hapmap]
rs4390325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417245	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4636650	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4756948	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757671	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757672	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56104322	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56138729	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56991251	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486434	0.84[YRI][hapmap]
rs6486435	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105889	0.84[YRI][hapmap]
rs7107057	0.84[YRI][hapmap]
rs72876754	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72876774	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7483340	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928872	0.80[YRI][hapmap]
rs7931630	0.80[YRI][hapmap]
rs7942733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6486431	TSG101	cis	multi-tissue	Pritchard
rs6486431	LDHC	cis	Muscle Skeletal	GTEx
rs6486431	LDHC	cis	parietal	SCAN
rs6486431	LDHC	cis	Nerve Tibial	GTEx
rs6486431	LDHC	cis	uninvolved skin	skin_eQTL
rs6486431	TSG101	cis	lymphoblastoid	seeQTL
rs6486431	LDHC	cis	Adipose Subcutaneous	GTEx
rs6486431	LDHC	cis	Artery Tibial	GTEx
rs6486431	RPS13	cis	parietal	SCAN
rs6486431	LDHC	cis	lymphoblastoid	seeQTL
rs6486431	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs6486431	LDHC	cis	cerebellum	SCAN
rs6486431	LDHC	cis	lung	GTEx
rs6486431	LDHC	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:18513000-18544000	Weak transcription	Gastric	stomach
3	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
4	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
6	chr11:18523800-18547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:18524200-18547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:18524200-18547400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:18527200-18547200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:18527600-18545400	Weak transcription	Small Intestine	intestine
11	chr11:18531200-18544600	Weak transcription	Hela-S3	cervix
12	chr11:18531400-18546600	Weak transcription	K562	blood
13	chr11:18532800-18547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:18533400-18547200	Weak transcription	A549	lung
15	chr11:18534800-18547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:18535000-18543400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:18535400-18547800	Weak transcription	Esophagus	oesophagus
18	chr11:18535600-18544000	Weak transcription	Spleen	Spleen
19	chr11:18535600-18544200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:18535600-18546600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:18535600-18547600	Weak transcription	Aorta	Aorta
22	chr11:18535800-18544000	Weak transcription	Left Ventricle	heart
23	chr11:18535800-18544000	Weak transcription	Ovary	ovary
24	chr11:18535800-18545800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:18535800-18546200	Weak transcription	Right Ventricle	heart
26	chr11:18535800-18547200	Weak transcription	HUVEC	blood vessel
27	chr11:18535800-18547400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:18535800-18547800	Weak transcription	Lung	lung
29	chr11:18536000-18543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:18536000-18544200	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:18536000-18546200	Weak transcription	Thymus	Thymus
32	chr11:18536200-18547200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:18536200-18547200	Weak transcription	HSMMtube	muscle
34	chr11:18536400-18544000	Weak transcription	HepG2	liver
35	chr11:18536400-18544200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:18536400-18545800	Weak transcription	GM12878-XiMat	blood
37	chr11:18536600-18547200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:18536800-18547400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:18537200-18545600	Weak transcription	NH-A	brain
40	chr11:18537200-18546800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:18537200-18547400	Weak transcription	Colonic Mucosa	Colon
42	chr11:18537400-18543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:18537400-18543800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:18537400-18544600	Weak transcription	NHEK	skin
45	chr11:18537400-18545600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:18537400-18546200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr11:18537400-18547200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:18537400-18547200	Weak transcription	Brain Angular Gyrus	brain
49	chr11:18537400-18547200	Weak transcription	Brain Substantia Nigra	brain
50	chr11:18537400-18547200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links